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- PDB-7o4x: Crystal structure of the PII-like protein PotN from Lentilactobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o4x | ||||||
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Title | Crystal structure of the PII-like protein PotN from Lentilactobacillus hilgardii | ||||||
![]() | Nitrogen regulatory protein P-II | ||||||
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Function / homology | ADENOSINE-5'-DIPHOSPHATE / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heim, C. / Hartmann, M.D. | ||||||
![]() | ![]() Title: PotN represents a novel energy-state sensing PII subfamily, occurring in firmicutes. Authors: Iskhakova, Z.I. / Zhuravleva, D.E. / Heim, C. / Hartmann, M.D. / Laykov, A.V. / Forchhammer, K. / Kayumov, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.4 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2eg1S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13759.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HMPREF0496_1931 / Production host: ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ADP / ![]() |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.56 M Tri-Na Citrate pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.65→40.11 Å / Num. obs: 18721 / % possible obs: 100 % / Redundancy: 26.19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.093 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 24.71 % / Rmerge(I) obs: 2.03 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2935 / CC1/2: 0.72 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2EG1 Resolution: 1.65→40.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.461 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.205 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→40.08 Å
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Refine LS restraints |
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